This distribution of pips (Phylogenetic Inference of Protein Stability) is the version that was used for the analyses in the paper "Inferring Stabilizing Mutations from Protein Phylogenies: Application to Influenza Hemagglutinin" by Jesse D. Bloom and Matthew J. Glassman in PLoS Computational Biology.  It contains the source code for all computational analyses in that paper.  This source code should work on all operating systems, but has only been tested on Mac OS X.  It requires the numpy and transcendental packages.

This distribution also contains (in the examples directory) the data and scripts used for the computational analyses in the aforementioned paper.  These scripts may require certain auxillary programs (alignment programs PROBCONS and MUSCLE, phylogeny program PHYLIP) which need to reside in directory locations that are hardcoded in the scripts.  They also require matplotlib/pylab.  These scripts therefore may not run on your computer without some manual editing.

The source code is extensively commented, but there is currently no general users manual.  A newer version of the pips program that is more user friendly and contains additional improved features is currently being developed.  This current version will be more useful to programmers than general users.  

You are free to use this software for non-commercial purposes, as described in the LICENSE.txt file.

If you have questions, you can contact Jesse Bloom at jesse.bloom@gmail.com.

To install the source code, type "python setup.py install".  You may need to be superuser in order to have permission to install the software on your computer.
